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You can map two different projects to two different instances of JIRA (or any other bug-tracker).
What you need to do is put two copies on the JiraDataSync DLL in the SpiraTest BIN folder.
E.g. call one JiraDataSync.dll and one JiraDataSync2.dll
Then in Administration > Data Synchronization create two plugin entries, one for JiraDataSync and one for JiraDataSync2. Then you can point each one at different instances of JIRA and map different projects to each of the providers.